The Protein Ontology (PRO) is designed as a formal and principled Open Biomedical Ontologies (OBO) Foundry ontology for proteins. The components of PRO extend from a classification of proteins on the basis of evolutionary relationships at the homeomorphic level to the representation of the multiple protein forms of a gene, including those resulting from alternative splicing, cleavage and/or posttranslational modifications. Focusing specifically on the TGF-beta signaling proteins, we describe the building, curation, usage and dissemination of PRO. PRO provides a framework (...) for the formal representation of protein classes and protein forms in the OBO Foundry. It is designed to enable data retrieval and integration and machine reasoning at the molecular level of proteins, thereby facilitating cross-species comparisons, pathway analysis, disease modeling and the generation of new hypotheses. (shrink)

Representing species-specific proteins and protein complexes in ontologies that are both human and machine-readable facilitates the retrieval, analysis, and interpretation of genome-scale data sets. Although existing protin-centric informatics resources provide the biomedical research community with well-curated compendia of protein sequence and structure, these resources lack formal ontological representations of the relationships among the proteins themselves. The Protein Ontology (PRO) Consortium is filling this informatics resource gap by developing ontological representations and relationships among proteins and their variants and modified forms. Because (...) proteins are often functional only as members of stable protein complexes, the PRO Consortium, in collaboration with existing protein and pathway databases, has launched a new initiative to implement logical and consistent representation of protein complexes. We describe here how the PRO Consortium is meeting the challenge of representing species-specific protein complexes, how protein complex representation in PRO supports annotation of protein complexes and comparative biology, and how PRO is being integrated into existing community bioinformatics resources. The PRO resource is accessible at http://pir.georgetown.edu/pro/. (shrink)

The Protein Ontology (PRO) provides a formal, logically-based classification of specific protein classes including structured representations of protein isoforms, variants and modified forms. Initially focused on proteins found in human, mouse and Escherichia coli, PRO now includes representations of protein complexes. The PRO Consortium works in concert with the developers of other biomedical ontologies and protein knowledge bases to provide the ability to formally organize and integrate representations of precise protein forms so as to enhance accessibility to results of protein (...) research. PRO (http://pir.georgetown.edu/pro) is part of the Open Biomedical Ontologies (OBO) Foundry. (shrink)

The Protein Ontology (PRO) web resource provides an integrative framework for protein-centric exploration and enables specific and precise annotation of proteins and protein complexes based on PRO. Functionalities include: browsing, searching and retrieving, terms, displaying selected terms in OBO or OWL format, and supporting URIs. In addition, the PRO website offers multiple ways for the user to request, submit, or modify terms and/or annotation. We will demonstrate the use of these tools for protein research and annotation.

The Protein Ontology (PRO; http://proconsortium.org) formally defines protein entities and explicitly represents their major forms and interrelations. Protein entities represented in PRO corresponding to single amino acid chains are categorized by level of specificity into family, gene, sequence and modification metaclasses, and there is a separate metaclass for protein complexes. All metaclasses also have organism-specific derivatives. PRO complements established sequence databases such as UniProtKB, and interoperates with other biomedical and biological ontologies such as the Gene Ontology (GO). PRO relates to (...) UniProtKB in that PRO’s organism-specific classes of proteins encoded by a specific gene correspond to entities documented in UniProtKB entries. PRO relates to the GO in that PRO’s representations of organism-specific protein complexes are subclasses of the organism-agnostic protein complex terms in the GO Cellular Component Ontology. The past few years have seen growth and changes to the PRO, as well as new points of access to the data and new applications of PRO in immunology and proteomics. Here we describe some of these developments. (shrink)

The Protein Ontology (PRO; http://purl.obolibrary.org/obo/pr) formally defines and describes taxon-specific and taxon-neutral protein-related entities in three major areas: proteins related by evolution; proteins produced from a given gene; and protein-containing complexes. PRO thus serves as a tool for referencing protein entities at any level of specificity. To enhance this ability, and to facilitate the comparison of such entities described in different resources, we developed a standardized representation of proteoforms using UniProtKB as a sequence reference and PSI-MOD as a post-translational modification (...) reference. We illustrate its use in facilitating an alignment between PRO and Reactome protein entities. We also address issues of scalability, describing our first steps into the use of text mining to identify protein-related entities, the large-scale import of proteoform information from expert curated resources, and our ability to dynamically generate PRO terms. Web views for individual terms are now more informative about closely-related terms, including for example an interactive multiple sequence alignment. Finally, we describe recent improvement in semantic utility, with PRO now represented in OWL and as a SPARQL endpoint. These developments will further support the anticipated growth of PRO and facilitate discoverability of and allow aggregation of data relating to protein entities. (shrink)

This work has been selected by scholars as being culturally important and is part of the knowledge base of civilization as we know it. This work is in the public domain in the United States of America, and possibly other nations. Within the United States, you may freely copy and distribute this work, as no entity (individual or corporate) has a copyright on the body of the work. Scholars believe, and we concur, that this work is important enough to be (...) preserved, reproduced, and made generally available to the public. To ensure a quality reading experience, this work has been proofread and republished using a format that seamlessly blends the original graphical elements with text in an easy-to-read typeface. We appreciate your support of the preservation process, and thank you for being an important part of keeping this knowledge alive and relevant. (shrink)

This work has been selected by scholars as being culturally important and is part of the knowledge base of civilization as we know it. This work is in the public domain in the United States of America, and possibly other nations. Within the United States, you may freely copy and distribute this work, as no entity (individual or corporate) has a copyright on the body of the work. Scholars believe, and we concur, that this work is important enough to be (...) preserved, reproduced, and made generally available to the public. To ensure a quality reading experience, this work has been proofread and republished using a format that seamlessly blends the original graphical elements with text in an easy-to-read typeface. We appreciate your support of the preservation process, and thank you for being an important part of keeping this knowledge alive and relevant. (shrink)

When the whole is greater than the sum of the parts--indeed, so great that the sum far transcends the parts and represents something utterly new and different--we call that phenomenon emergence. When the chemicals diffusing in the primordial waters came together to form the first living cell, that was emergence. When the activities of the neurons in the brain result in mind, that too is emergence. In The Emergence of Everything, one of the leading scientists involved in the study of (...) complexity, Harold J. Morowitz, takes us on a sweeping tour of the universe, a tour with 28 stops, each one highlighting a particularly important moment of emergence. For instance, Morowitz illuminates the emergence of the stars, the birth of the elements and of the periodic table, and the appearance of solar systems and planets. We look at the emergence of living cells, animals, vertebrates, reptiles, and mammals, leading to the great apes and the appearance of humanity. He also examines tool making, the evolution of language, the invention of agriculture and technology, and the birth of cities. And as he offers these insights into the evolutionary unfolding of our universe, our solar system, and life itself, Morowitz also seeks out the nature of God in the emergent universe, the God posited by Spinoza, Bruno, and Einstein, a God Morowitz argues we can know through a study of the laws of nature. Written by one of our wisest scientists, The Emergence of Everything offers a fascinating new way to look at the universe and the natural world, and it makes an important contribution to the dialogue between science and religion. (shrink)

The following argument is presented and defended: We ought to aspire to become as good as we can be, and this requires that we do good deeds with not just any emotional attitude, but with joy (a lively, hopeful feeling), even in difficult circumstances. Theism (of the right sort) offers us the best prospects for achieving a fully joyful moral life. And so it is morally good for those of us who are not theists to undertake theism-to commit ourselves to (...) the religious project of coming to believe that God exists. (shrink)

Introduction Gramsci's relevance The name of the late Italian Marxist, Antonio Gramsci, appears increasingly in the cultural media of the English- speaking ...

Professor Brown describes and criticises the major classical model of rationality and offers a new model of this central concept in the history of philosophy and of science.

Revolutionizing received opinion of Taoism's origins in light of historic new discoveries, Harold D. Roth has uncovered China's oldest mystical text--the original expression of Taoist philosophy--and presents it here with a complete translation and commentary. Over the past twenty-five years, documents recovered from the tombs of China's ancient elite have sparked a revolution in scholarship about early Chinese thought, in particular the origins of Taoist philosophy and religion. In _Original Tao,_ Harold D. Roth exhumes the seminal text of (...) Taoism--_Inward Training (Nei-yeh)_--not from a tomb but from the pages of the _Kuan Tzu,_ a voluminous text on politics and economics in which this mystical tract had been "buried" for centuries. _Inward Training_ is composed of short poetic verses devoted to the practice of breath meditation, and to the insights about the nature of human beings and the form of the cosmos derived from this practice. In its poetic form and tone, the work closely resembles the _Tao-te Ching_; moreover, it clearly evokes Taoism's affinities to other mystical traditions, notably aspects of Hinduism and Buddhism. Roth argues that _Inward Training_ is the foundational text of early Taoism and traces the book to the mid-fourth century B.C. (the late Warring States period in China). These verses contain the oldest surviving expressions of a method for mystical "inner cultivation," which Roth identifies as the basis for all early Taoist texts, including the _Chuang Tzu_ and the world-renowned _Tao-te Ching._ With these historic discoveries, he reveals the possibility of a much deeper continuity between early "philosophical" Taoism and the later Taoist religion than scholars had previously suspected. _Original Tao_ contains an elegant and luminous complete translation of the original text. Roth's comprehensive analysis explains what _Inward Training_ meant to the people who wrote it, how this work came to be "entombed" within the _Kuan Tzu,_ and why the text was largely overlooked after the early Han period. (shrink)

This paper considers two reasons that might support Russell’s choice of a ramified-type theory over a simple-type theory. The first reason is the existence of purported paradoxes that can be formulated in any simple-type language, including an argument that Russell considered in 1903. These arguments depend on certain converse-compositional principles. When we take account of Russell’s doctrine that a propositional function is not a constituent of its values, these principles turn out to be too implausible to make these arguments troubling. (...) The second reason is conditional on a substitutional interpretation of quantification over types other than that of individuals. This reason stands up to investigation: a simple-type language will not sustain such an interpretation, but a ramified-type language will. And there is evidence that Russell was tacitly inclined towards such an interpretation. A strong construal of that interpretation opens a way to make sense of Russell’s simultaneous repudiation of propositions and his willingness to quantify over them. But that way runs into trouble with Russell’s commitment to the finitude of human understanding. (shrink)

During the 1992–1993 academic year, Harold Garfinkel offered a graduate seminar on Ethnomethodology in the Sociology Department at the University of California, Los Angeles. One topic that was given extensive coverage in the seminar has not been discussed at much length in Garfinkel’s published works to date: Aron Gurwitsch’s treatment of Gestalt theory, and particularly the themes of “phenomenal field” and “praxeological description”. The edited transcript of Garfinkel’s seminar shows why he recommended that “for the serious initiatives of ethnomethodological (...) investigations […] Gurwitsch is a theorist we can’t do without”. Garfinkel’s ethnomethodological “misreading” is not a mistaken reading, but is more a matter of taking Gurwitsch’s phenomenological demonstrations of Gestalt contextures in phenomenal fields and transposing them for making detailed, concrete observations and descriptions of organizationally achieved social phenomena. Where Gurwitsch addresses the organization of perception as an autochthonous achievement, inherent to the stream and field of individual consciousness, Garfinkel extends and elaborates this field into the social world of enacted practices. The April 1993 seminar also is rich with brief asides and digressions in which Garfinkel comments about his use of Alfred Schutz, his attitude toward publishing, his relationship with Erving Goffman, and many other matters. (shrink)

Editors’ AbstractDuring the 1992–1993 academic year, Harold Garfinkel (1917–2011) offered a graduate seminar on Ethnomethodology in the Sociology Department at the University of California, Los Angeles. One topic that was given extensive coverage in the seminar has not been discussed at much length in Garfinkel’s published works to date: Aron Gurwitsch’s treatment of Gestalt theory, and particularly the themes of “phenomenal field” and “praxeological description”. The edited transcript of Garfinkel’s seminar shows why he recommended that “for the serious initiatives (...) of ethnomethodological investigations […] Gurwitsch is a theorist we can’t do without”. Garfinkel’s ethnomethodological “misreading” is not a mistaken reading, but is more a matter of taking Gurwitsch’s phenomenological demonstrations of Gestalt contextures in phenomenal fields and transposing them for making detailed, concrete observations and descriptions of organizationally achieved social phenomena. Where Gurwitsch addresses the organization of perception as an autochthonous achievement, inherent to the stream and field of individual consciousness, Garfinkel extends and elaborates this field into the social world of enacted practices. The April 1993 seminar also is rich with brief asides and digressions in which Garfinkel comments about his use of Alfred Schutz, his attitude toward publishing, his relationship with Erving Goffman, and many other matters. (shrink)

Revolutionizing received opinion of Taoism's origins in light of historic new discoveries, Harold D. Roth has uncovered China's oldest mystical text -- the original expression of Taoist philosophy -- and presents it here with a complete translation and commentary. Over the past twenty-five years, documents recovered from the tombs of China's ancient elite have sparked a revolution in scholarship about early Chinese thought, in particular the origins of Taoist philosophy and religion. In _Original Tao,_ Harold D. Roth exhumes (...) the seminal text of Taoism -- _Inward Training _ -- not from a tomb but from the pages of the _Kuan Tzu,_ a voluminous text on politics and economics in which this mystical tract had been "buried" for centuries. _Inward Training_ is composed of short poetic verses devoted to the practice of breath meditation, and to the insights about the nature of human beings and the form of the cosmos derived from this practice. In its poetic form and tone, the work closely resembles the _Tao-te Ching_; moreover, it clearly evokes Taoism's affinities to other mystical traditions, notably aspects of Hinduism and Buddhism. Roth argues that _Inward Training_ is the foundational text of early Taoism and traces the book to the mid-fourth century B.C.. These verses contain the oldest surviving expressions of a method for mystical "inner cultivation," which Roth identifies as the basis for all early Taoist texts, including the _Chuang Tzu_ and the world-renowned _Tao-te Ching._ With these historic discoveries, he reveals the possibility of a much deeper continuity between early "philosophical" Taoism and the later Taoist religion than scholars had previously suspected. _Original Tao_ contains an elegant and luminous complete translation of the original text. Roth's comprehensive analysis explains what _Inward Training_ meant to the people who wrote it, how this work came to be "entombed" within the _Kuan Tzu,_ and why the text was largely overlooked after the early Han period. (shrink)

It is generally not recognized that Whewell's conception of necessary truth evolved only gradually; his early statements are misleading. For this reason, and because of certain peculiarities in his expository style over his publishing history, he is commonly thought to have used the term "necessary" in the sense of "absolutely necessary". I argue that, on the contrary, the term is essentially relational in his mature view. This conclusion leads, in turn, to a re-interpretation of his doctrine of "fundamental ideas". Here (...) I argue that the crux of his position is that cognitive principles which are initially regulative become, through invention, repeated employment, and stipulative definition, constitutive ones. (shrink)

The platonist who argues that the moral life has no religious implications is mistaken. If one ought to aspire to become as good as one can become, then, since the identity of this goal depends in part on whether or not it is possible to enter into a conscious, loving relation with God, one ought to try to figure out whether or not God exists. But then one needs to get a clearer understanding of what it is to be God. (...) So one ought to turn one's attention to what it is to be God. (shrink)